Conformational changes in fragments D and double-D from human fibrin(ogen) upon binding the peptide ligand Gly-His-Arg-Pro-amide

Biochemistry. 1999 Mar 9;38(10):2941-6. doi: 10.1021/bi982626w.

Abstract

The structure of fragment double-D from human fibrin has been solved in the presence and absence of the peptide ligands that simulate the two knobs exposed by the removal of fibrinopeptides A and B, respectively. All told, six crystal structures have been determined, three of which are reported here for the first time: namely, fragments D and double-D with the peptide GHRPam alone and double-D in the absence of any peptide ligand. Comparison of the structures has revealed a series of conformational changes that are brought about by the various knob-hole interactions. Of greatest interest is a moveable "flap" of two negatively charged amino acids (Glubeta397 and Aspbeta398) whose side chains are pinned back to the coiled coil with a calcium atom bridge until GHRPam occupies the beta-chain pocket. Additionally, in the absence of the peptide ligand GPRPam, GHRPam binds to the gamma-chain pocket, a new calcium-binding site being formed concomitantly.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Binding Sites
  • Calcium / physiology
  • Calcium-Binding Proteins / metabolism
  • Computer Simulation
  • Crystallization
  • Crystallography, X-Ray
  • Fibrin Fibrinogen Degradation Products / chemistry*
  • Fibrin Fibrinogen Degradation Products / metabolism*
  • Humans
  • Ligands
  • Models, Molecular
  • Oligopeptides / metabolism*
  • Peptide Fragments / chemistry
  • Protein Binding
  • Protein Conformation

Substances

  • Calcium-Binding Proteins
  • Fibrin Fibrinogen Degradation Products
  • Ligands
  • Oligopeptides
  • Peptide Fragments
  • fibrinogen D fragment
  • glycyl-histidyl-arginyl-proline
  • Calcium

Associated data

  • PDB/1FZE
  • PDB/1FZF
  • PDB/1FZG